On 26 August 2006, Lonergan suffered serious internal injury to his kidney whilst playing in a Round 21 draw against Melbourne - which was also just his seventh AFL-level match.[3] Lonergan's kidney was severely damaged when he backed into a marking contest against Melbourne's Brad Miller.[3]

Lonergan was immediately hospitalised, taken to the Geelong Hospital and had been in a stable condition before his blood pressure rose overnight,[4] forcing him to undergo trauma surgery to remove his right kidney.[3] His kidney was found to be badly lacerated and bruised, which was accentuated by the scar tissue caused by a previous footballing injury he had suffered as a 16-year-old.[3] During the six-hour procedure, Lonergan's entire blood supply had to be replaced three times, flushing it through with up to 40 units of blood,[5] placing him into an induced coma.[3][6] Lonergan remained in a coma for four days, with it taking six hours to bring him back to consciousness.[7] He also lost 17 kg during the ordeal.[8]

Lonergan decided to continue his AFL career, after considering premature retirement, with Geelong agreeing to delist Lonergan, but then re-draft him via the Rookie Draft,[9][10][11] with Geelong hoping that other clubs would avoid drafting Lonergan due to the extent of his injuries.[9] Lonergan believed the outcome would benefit both the club and himself,[9] with the club able to draft a new talented youngster through the National Draft, and himself able to continue his recovery at a stable rate.[9] The club is reported to have taken this decision to help Lonergan if he wished to continue his career. Lonergan himself considered retirement following the surgery, but opted to return. Club doctor Chris Bradshaw compared Lonergan's efforts to return to professional sport with those of Jason McCartney, who was injured in the 2002 Bali Bombing before playing one final game.[6]

The day after being re-drafted by Geelong, Lonergan was again involved in another potentially life-threatening incident, this time in the form of a serious car accident.[11] The accident occurred when Lonergan was driving to training, and another car careered into his passenger-side door and pushed him into oncoming traffic.[11] He was lucky to escape with just a scratched leg, but the accident did write off his car.[11] This was another chapter in Lonergan's run of bad luck, with his car getting broken into just a week and a half before the accident.[11] Lonergan stated to the media that he hoped his bad luck had finally come to an end, and jokingly attributed the bad luck to the fact he wore the "unlucky" number 13.[11]

Lonergan made his return to the sport on June 17, 2007, playing for Geelong's VFL team against Tasmania. He played the second half of each quarter, kicking one behind, as well as marking five times and making ten disposals. Speaking to reporters after the match, he indicated that he had no time-line for returning to the top league, but fully intended to do so.[12] He had previously remarked on the unusual nature of his injury, claiming that it was a very different feeling to having damaged a joint or a limb.[8]

To cap a fairytale return to football Lonergan played in the 126-52 VFL Grand Final win over the Coburg Tigers kicking six goals[1] earning him the Norm Goss Memorial Medal for best on ground. As a result of his strong form and full recovery from his injuries, Lonergan was elevated to Geelong's senior list for the 2008 AFL Premiership Season.

Lonergan was the recipient of the club's Community Champion award, presented at the club's Best and Fairest dinner.[13][14]

Lonergan played in the Geelong team in the 2008 AFL Grand Final, and missed selection into the Geelong 2009 premiership team. However, during 2011 Tom became a key member of Geelong's defensive back six players, and played a critical role in the 2011 AFL Grand Final holding Travis Cloke goalless in the second half, after Cloke had kicked three goals early in the game while playing on Harry Taylor.[15] The job he executed was crucial for the Cats as it helped stemmed the flow of Collingwood goals and took the red-hot Cloke out of the game.[16]

During the 2014 AFL trade period, Lonergan was offered a three-year contract to join the Western Bulldogs, in a deal estimated to be worth $500,000 a season.[17] Lonergan, who was already contracted to Geelong for 2015,[17] ultimately rejected the offer, citing loyalty to his teammates and the resignation of the Western Bulldogs' coach Brendan McCartney as his main reasons for remaining with the club.[18] Subsequently, Geelong have reportedly extended Lonergan's contract until the end of the 2016 season.[17]

Following his injuries, Lonergan became an ambassador for Zaidee's Rainbow Foundation, an organisation raising awareness of organ donation. The Geelong senior side wore rainbow-coloured laces (the symbol of the foundation) in their boots during their match against the Brisbane Lions immediately following Lonergan's VFL match.[8] Lonergan was in fact wearing rainbow laces during the match in which he was injured.[19]

He is the youngest son of Trish and Bernie (Stump) Longergan, who still live in Yarrawonga. He has two brothers and a sister.[1]